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PhyloBayes MPI on XSEDE (v 1.4f)

PhyloBayes (Lartillot et al, 2009) is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction. The main distinguishing feature of PhyloBayes is its use of the underlying probabilistic model, CAT (Lartillot and Philippe, 2004). CAT is an infinite mixture model accounting for site-specific amino-acid or nucleotide preferences. It is well suited to phylogenomic studies using large multigene alignments, as it allows selection to be evaluated separately for each position in a sequence..

PhlyoBayes MPI on XSEDE provides a primitive interface that submits jobs to Gordon, a large NSF XSEDE Resource. Please contact us if you have trouble using the interface.

PhyloBayes MPI supports checkpointing, which makes it possible to restart a run that has terminated unexpectedly, or that has reached the end of the maximum allowed run time without converging.

Manual for PhyloBayes MPI 1.4f (pdf); Supplement (pdf)

PhyloBayes MPI home page here.

INPUT = dna or protein matrices in relaxed Phylip format

OUTPUT = A set of files the most important of which are:

• <name>.chain: this file contains the detailed parameter configurations visited during the run and is used by readpb_mpi for computing posterior averages.
• <name>.treelist: list of sampled trees
• <name>.trace: the trace file, containing a few relevant summary statistics (log-likelihood, total length of the tree, number of components in the mixture, etc).
• <name>.param a parameter file that is required for restarting a chain (see the restart help page). .

If there is a tool or a feature you need, Please let us know.